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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

AnalyzeCovariates

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2 comments

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    Lucas Kopecky Bobadilla

    I actually figure it out by running the R script alone. It seems that it is needed to transform the csv file strings to factor.

     

    By adding changing the line 16 from:

    data <- read.csv(args[1])

    to

    data <- read.csv(args[1], stringsAsFactors = TRUE)

    The R script worked. Any chance to change the script so this error stop to occur in the future?

     

    Thanks!

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    Bhanu Gandham

    Hi Lucas Kopecky Bobadilla

     

    Thank you for pointing out this issue and for helping us find a solution for it. I have created a issue ticket for this and you can follow its progress here: https://github.com/broadinstitute/gatk/issues/6650

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